The application of robotics and mass spectrometry to the characterisation of the Drosophila melanogaster indirect flight muscle proteome

The rapid accumulation of sequence data generated by the various genome sequencing projects and the generation of expressed sequence tag databases has resulted in the need for the development of fast and sensitive methods for the identification and characterisation of large numbers of gel electrophoretically separated proteins to translate the sequence data into biological function, To achieve this goal it has been necessary to devise new approaches to protein analysis: matrix-assisted laser desorption and electrospray mass spectrometry have become important protein analytical tools which are both fast and sensitive. When combined with a robotic system for the in-gel digestion of electrophoretically separated proteins, it becomes possible to rapidly identify many proteins by searching databases with MS data. The power of this combination of techniques is demonstrated by an analysis of the proteins present in the myofibrillar lattice of the indirect flight muscle of Drosophila melanogaster. The proteins were separated by SDS-PAGE and in-gel proteolysis was performed both automatically and manually. All 16 major proteins could quickly be identified by mass spectrometry. Although most of the protein components were known to be present in the flight muscle, two new components were also identified. The combination of methods described offers a means for the rapid identification of large numbers of gel separated proteins.